Ok, first to clear up your last questions. Yes, in Schtrom 3.2 the ISO is used instead of the .000, but when actually burning with ImgBurn (thats what i use anyway) you select the .dvd file.
So, in summary, you do your converting with nmeaSSociator to the ISO file (or .000 if using an older version of Schtrom), then you select the .dvd file when burning with ImgBurn.
Now, as far as your other problem, it definately sounds like the disc. A scratched disc will result in you getting a message somewhere along the lines of "Cant read, replace sectors with 0?, this WONT happen on Xbox 360 games" or something like that.
Xbox Backup Creator might be a slightly better option for those games that are scratched, because it has the ability to "retry" reading the sectors. So, for instance, if the game skips when trying to read or is scratched, XBC gives you the option to re-read the missing/scratched file.
Now, about why Juarez wont play, I honestly cant give you a straight answer, because it could be a number of things. Like maybe a bad burn, bad disc, your Xbox 360 dvd drive laser may be crapping out a little, etc....